Applying meta-data of soybean grain in origin trace and quarantine inspection

•We characterized the soybean-grain associated bacterial and fungal communities of world's largest soybean-producing countries (China, United States of America, Brazil, and Argentina).•Our results showed that the soybean-associated microbiota from different continents significantly separated, presenting strong geographic variations. The core microbial taxa and geographically specified taxa were defined.•We build the Random Forest (RF) model to predict the source of imported soybean grains. We could accurately predict the original countries of imported soybean grains within the RF prediction model, with an accuracy greater than 95%.•We constructed a soybean-related quarantine pathogens database using full-length sequences of fungal ITS region and bacterial 16S rDNA. Based on this database, two phytopathogenic fungi, Diaporthe caulivora, and Cladosporium cucumerinum, listed in the China quarantine catalog, were intercepted through metabarcoding sequencing.